Compensatory effects in the PI3K/PTEN/AKT signaling network following receptor tyrosine kinase inhibition

Overcoming de novo and acquired resistance to anticancer drugs that target signaling networks is a formidable challenge for drug design and effective cancer therapy. Understanding the mechanisms by which this resistance arises may offer a route to addressing the insensitivity of signaling networks to drug intervention and restore the efficacy of anticancer therapy. Extending our recent work identifying PTEN as a key regulator of Herceptin sensitivity, we present an integrated theoretical and experimental approach to study the compensatory mechanisms within the PI3K/PTEN/AKT signaling network that afford resistance to receptor tyrosine kinase (RTK) inhibition by anti-HER2 monoclonal antibodies. In a computational model representing the dynamics of the signaling network, we define a single control parameter that encapsulates the balance of activities of the enzymes involved in the PI3K/PTEN/AKT cycle. By varying this control parameter we are able to demonstrate both distinct dynamic regimes of behavior of the signaling network and the transitions between those regimes. We demonstrate resistance, sensitivity, and suppression of RTK signals by the signaling network. Through model analysis we link the sensitivity-to-resistance transition to specific compensatory mechanisms within the signaling network. We study this transition in detail theoretically by variation of activities of PTEN, PI3K, AKT enzymes, and use the results to inform experiments that perturb the signaling network using combinatorial inhibition of RTK, PTEN, and PI3K enzymes in human ovarian carcinoma cell lines. We find good alignment between theoretical predictions and experimental results. We discuss the application of the results to the challenges of hypersensitivity of the signaling network to RTK signals, suppression of drug resistance, and efficacy of drug combinations in anticancer therapy.     

Relationship between radiation induced adaptive response in human fibroblasts and changes in chromatin conformation

Chromatin conformation changes in the normal human fibroblasts VH-10 were studied by the method of anomalous viscosity time dependence (AVTD). Gamma-irradiation of cells in a dose range of 0.1–3 Gy caused an increase in maximal viscosity of cell lysates. Conversely, irradiation of cells with low doses of 0.5 or 2 cGy resulted in a decrease in the AVTD peaks with a maximum effect approximately 40 min after irradiation. The same exposure conditions were used to study a possible adaptive effect of low doses, measured by changes in cell survival. A primary dose of 2 cGy caused significant modification of cell response to a challenge dose. Approximately 20% protection to challenge doses of 0.5 Gy (p < 0.003), 2 Gy (p < 0.02) and 2.5 Gy (p < 0.002) was observed. However, the direction of this effect (adaptation or synergism) was found to be dependent on a challenge dose. The combined effect of 2 cGy and 1 Gy was significantly synergistic, while no modification was observed for 1.5 Gy and 3 Gy. A partial correlation was found between the AVTD changes and cell survival when the combined effect of a primary dose of 2 cGy and challenge dose was examined. The dose of 2 cGy alone increased survival by 16% (p < 0.0003). These results suggest that the low-dose induced effects on survival may be related to chromatin reorganization.     

Membranotropic effects of peptides from the V3 loop of HIV-1

The V3 loop from HIV-1 envelope glycoprotein gp120 is involved in viral entry and determines the cellular tropism and HIV-1-induced cell–cell fusion. Earlier we have shown that V3 loop peptides representing the sequences of syncytia-inducing HIV strains have high membranotropic activity. These peptides caused the lysis of liposomes of various lipid compositions, could fuse negatively charged liposomes and induced hemolysis of erythrocytes. In contrast, peptides mimicking the sequences of non-syncytia-inducing viruses showed no lytic or fusion activities at the same concentrations. Now we have found that the V3 loop synthetic peptides containing the conserved GPGR region, derived from T-lymphotropic strains (BRU and MN), as opposed to peptides containing the GPGQ region, are able to cause a pronounced membrane permeabilization (dissipation of the pH and the of human peripheral blood lymphocytes, erythrocytes and plasma membrane vesicles at micromolar concentrations with a dose-dependent kinetics. Analysis of the secondary structures of the peptides by circular dichroism revealed conformational changes in V3 loop peptides depending on solvent hydrophobicity: from random coil in water to an -helix/-sheet conformation in trifluoroethanol. Such structural changes of the V3 loop together with the membrane insertion of the gp41 N-terminal fusion peptide may promote the formation of the fusion pore during virus–cell fusion.     

The integripennis species group of Geocharidius Jeannel, 1963 (Carabidae,Bembidiini, Anillina) from Nuclear Central America: a taxonomic review with notes about biogeography and speciation

Our review recognizes 15 species of the integripennis species group of Geocharidius from Nuclear Central America, include three species previously described (Geocharidius gimlii Erwin, Geocharidius integripennis (Bates) and Geocharidius zullinii Vigna Taglianti) and 12 described here as new. They are: Geocharidius andersoni sp. n. (type locality: Chiapas, Chiapas Highlands, Cerro Huitepec) and Geocharidius vignatagliantii sp. n. (type locality: Chiapas, Motozintla, Sierra Madre de Chiapas, Benito Juárez) from Mexico; Geocharidius antigua sp. n. (type locality: Sacatepéquez, 5 km SE of Antigua), Geocharidius balini sp. n. (type locality: Suchitepéquez, 4 km S of Volcan Atitlán), Geocharidius erwini sp. n. (type locality: Quiché Department, 7 km NE of Los Encuentros), Geocharidius jalapensis sp. n. (type locality: Jalapa Department, 4 km E of Mataquescuintla), Geocharidius longinoi, sp. n. (type locality: El Progreso Department, Cerro Pinalón), and Geocharidius minimus sp. n. (type locality: Sacatepéquez Department, 5 km SE of Antigua) from Guatemala; and Geocharidius celaquensis sp. n. (type locality: Lempira Department, Celaque National Park), Geocharidius comayaguanus sp. n. (type locality: Comayagua Department, 18 km ENE of Comayagua), Geocharidius disjunctus sp. n. (type locality: Francisco Morazán, La Tigra National Park), and Geocharidius lencanus sp. n. (type locality: Lempira Department, Celaque National Park) from Honduras. For all members of the group, adult structural characters, including male and female genitalia, are described, and a taxonomic key for all members of the integripennis species group is presented based on these characters. Behavioral and biogeographical aspects of speciation in the group are discussed, based on the morphological analysis. In all cases of sympatry, pairs of closely related species show greater differences in sizes than pairs of more remotely related species. Integripennis group species occupy six different montane areas at elevations above 1300m, with no species shared among them. Major faunal barriers in the region limiting present species distributions include the Motagua Fault Zone and a gap between the Guatemalan Cordillera volcanic chain and the Honduran Interior Highlands no higher than 900m in elevation. Highest species diversity is in the Guatematan Cordillera (six species), second highest in the Honduran Interior Highlands area (four species).     

Prevalence of intron gain over intron loss in the evolution of paralogous gene families

The mechanisms and evolutionary dynamics of intron insertion and loss in eukaryotic genes remain poorly understood. Reconstruction of parsimonious scenarios of gene structure evolution in paralogous gene families in animals and plants revealed numerous gains and losses of introns. In all analyzed lineages, the number of acquired new introns was substantially greater than the number of lost ancestral introns. This trend held even for lineages in which vertical evolution of genes involved more intron losses than gains, suggesting that gene duplication boosts intron insertion. However, dating gene duplications and the associated intron gains and losses based on the molecular clock assumption showed that very few, if any, introns were gained during the last ~100 million years of animal and plant evolution, in agreement with previous conclusions reached through analysis of orthologous gene sets. These results are generally compatible with the emerging notion of intensive insertion and loss of introns during transitional epochs in contrast to the relative quiet of the intervening evolutionary spans.     

Genetic targeting of Card19 is linked to disrupted NINJ1 expression,impaired cell lysis,and increased susceptibility to Yersinia infection

Cell death plays a critical role in inflammatory responses. During pyroptosis, inflammatory caspases cleave Gasdermin D (GSDMD) to release an N-terminal fragment that generates plasma membrane pores that mediate cell lysis and IL-1 cytokine release. Terminal cell lysis and IL-1β release following caspase activation can be uncoupled in certain cell types or in response to particular stimuli, a state termed hyperactivation. However, the factors and mechanisms that regulate terminal cell lysis downstream of GSDMD cleavage remain poorly understood. In the course of studies to define regulation of pyroptosis during Yersinia infection, we identified a line of Card19-deficient mice (Card19^lxcn) whose macrophages were protected from cell lysis and showed reduced apoptosis and pyroptosis, yet had wild-type levels of caspase activation, IL-1 secretion, and GSDMD cleavage. Unexpectedly, CARD19, a mitochondrial CARD-containing protein, was not directly responsible for this, as an independently-generated CRISPR/Cas9 Card19 knockout mouse line (Card19^Null) showed no defect in macrophage cell lysis. Notably, Card19 is located on chromosome 13, immediately adjacent to Ninj1, which was recently found to regulate cell lysis downstream of GSDMD activation. RNA-seq and western blotting revealed that Card19^lxcn BMDMs have significantly reduced NINJ1 expression, and reconstitution of Ninj1 in Card19^lxcn immortalized BMDMs restored their ability to undergo cell lysis in response to caspase-dependent cell death stimuli. Card19^lxcn mice exhibited increased susceptibility to Yersinia infection, whereas independently-generated Card19^Null mice did not, demonstrating that cell lysis itself plays a key role in protection against bacterial infection, and that the increased infection susceptibility of Card19^lxcn mice is attributable to loss of NINJ1. Our findings identify genetic targeting of Card19 being responsible for off-target effects on the adjacent gene Ninj1, disrupting the ability of macrophages to undergo plasma membrane rupture downstream of gasdermin cleavage and impacting host survival and bacterial control during Yersinia infection.     

Quantitative detection of (125)IdU-induced DNA double-strand breaks with gamma-H2AX antibody

When mammalian cells are exposed to ionizing radiation and other agents that introduce DSBs into DNA, histone H2AX molecules in megabase chromatin regions adjacent to the breaks become phosphorylated within minutes on a specific serine residue. An antibody to this phosphoserine motif of human H2AX (gamma-H2AX) demonstrates that gamma-H2AX molecules appear in discrete nuclear foci. To establish the quantitative relationship between the number of these foci and the number of DSBs, we took advantage of the ability of (125)I, when incorporated into DNA, to generate one DNA DSB per radioactive disintegration. SF-268 and HT-1080 cell cultures were grown in the presence of (125)IdU and processed immunocytochemically to determine the number of gamma-H2AX foci. The numbers of (125)IdU disintegrations per cell were measured by exposing the same immunocytochemically processed samples to a radiation-sensitive screen with known standards. Under appropriate conditions, the data yielded a direct correlation between the number of (125)I decays and the number of foci per cell, consistent with the assumptions that each (125)I decay yields a DNA DSB and each DNA DSB yields a visible gamma-H2AX focus. Based on these findings, we conclude that gamma-H2AX antibody may form the basis of a sensitive quantitative method for the detection of DNA DSBs in eukaryotic cells.     

The point of maximum cell water volume excursion in case of presence of an impermeable solute

A relativistic permeability model of cell osmotic response (Cryobiology 40:64-83; 41:366-367) is applied to a two-solute system with one impermeable solute. The use of the normalized water volume (w), and the amount of intracellular permeable solute (x), which is the product of the water volume and intracellular osmolality (y), as the main variables allowed us to obtain a homogeneous differential equation dx(Delta)/dw(Delta)=f(x(Delta)/w(Delta)), where w(Delta)=w-w(f), x(Delta)=x-x(f), and f refers to the final (equilibrium) values. The solution of this equation is an explicit function, w(Delta)=g(x(Delta)), which is given in the text. This approach allows us to obtain an analytical (exact) expression of the water volume at the moment of the maximum excursion (water extremum w(m)). Results are compared with numeration of basic osmotic equations and with approximation given in (Cryobiology 40:64-83). Assumption that, dw/dt approximately 0 gives good approximations of the kinetics of water and permeable CPA after the point of maximum volume excursion (the slow phase of osmotic response). Practical aspects of the relativistic permeability approach are also discussed.